DNA Methylation and Transcriptomic Next-Generation Technologies in Cereal Genomics

Methods Mol Biol. 2020:2072:65-84. doi: 10.1007/978-1-4939-9865-4_7.

Abstract

RNA sequencing (RNA-seq) coupled to DNA methylation strategies enables the detection and characterization of genes which expression levels might be mediated by DNA methylation. Here we describe a bioinformatics protocol to analyze gene expression levels using RNA-seq data that allow us to identify candidate genes to be tested by bisulfite assays. The candidate methylated genes are usually those that are low expressed in a particular condition or developmental stage.

Keywords: Bioinformatics; Bisulfite technique; Cereals; Genome methylation; Transcriptome expression.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology / methods
  • DNA Methylation*
  • Databases, Genetic
  • Edible Grain / genetics*
  • Gene Expression Profiling* / methods
  • Gene Expression Profiling* / standards
  • Genomics* / methods
  • High-Throughput Nucleotide Sequencing* / methods
  • High-Throughput Nucleotide Sequencing* / standards
  • Humans
  • Sequence Analysis, DNA / methods
  • Software
  • Transcriptome*
  • Zea mays / genetics